Re: [AMBER] A clear procedure to do WHAM based on the REMD simulations outputs

From: Daniel Sindhikara <>
Date: Tue, 27 Jul 2010 20:15:10 +0900

   You can either develop your own code, or use someone else's such as:
Alan Grossfields:
John Chodera's:

Someone else might have a "more straightforward" way of doing this.
I use my own code, but in its current condition I couldn't lend it out *yet*in
full conscience. :P

On Tue, Jul 27, 2010 at 7:43 AM, Dongshan Wei <> wrote:

> Hi Everyone,
> Recently I want to do a ramachandran plot for an Alanine peptide. I
> did a 10ns temperature REMD simulations with 16 replicas. Now I want
> to weight the probability for temperatures not at T0 to get the
> weighted ramachandran plot. I made a quick look through the mailing
> list and find most WHAM is combined with umbrella sampling. Can
> somebody give a clear procedure on how to do WHAM based on REMD
> simulations outputs?
> Thanks so much!
> Dongshan
> _______________________________________________
> AMBER mailing list

Dr. Daniel J. Sindhikara
Institute for Molecular Science
AMBER mailing list
Received on Tue Jul 27 2010 - 04:30:03 PDT
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